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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| name: "conda_cron" | ||
| on: | ||
| workflow_dispatch: | ||
| schedule: | ||
| # At 07:00 UTC every day | ||
| - cron: "0 7 * * *" | ||
|
|
||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.ref }}" | ||
| cancel-in-progress: true | ||
|
|
||
| defaults: | ||
| run: | ||
| shell: bash -leo pipefail {0} | ||
|
|
||
| jobs: | ||
| condacheck: | ||
| runs-on: ${{ matrix.OS }} | ||
| name: "daily conda check" | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: ['ubuntu-latest', 'macos-latest', 'macos-12'] | ||
| python-version: | ||
| - "3.9" | ||
| - "3.10" | ||
| - "3.11" | ||
| - "3.12" | ||
| exclude: | ||
| - os: 'macos-latest' | ||
| python-version: '3.9' | ||
|
|
||
| steps: | ||
| - name: Setup Micromamba | ||
| uses: mamba-org/setup-micromamba@v1 | ||
| with: | ||
| micromamba-version: '1.5.6-0' | ||
| micromamba-binary-path: ~/.local/bin/micromamba | ||
| environment-name: openfe | ||
| create-args: >- | ||
| python=${{ matrix.python-version }} | ||
| pip | ||
| jq | ||
| condarc: | | ||
| channels: | ||
| - jaimergp/label/unsupported-cudatoolkit-shim | ||
| - conda-forge | ||
| init-shell: bash | ||
|
|
||
| - name: "Install openfe + optional deps" | ||
| run: | | ||
| # get latest version from conda-forge | ||
| LATEST_VERSION=$(micromamba search --json openfe | jq '.result.pkgs[0].version') | ||
| echo "LATEST_VERSION: $LATEST_VERSION" | ||
| # Removing the quotes from the vesrion number | ||
| # https://mywiki.wooledge.org/BashGuide/Parameters#Parameter_Expansion | ||
| micromamba install openfe=${LATEST_VERSION//\"} pytest -c conda-forge | ||
| python -m pip install pytest-xdist | ||
| - name: "env info" | ||
| run: | | ||
| micromamba info | ||
| micromamba list | ||
| pip list | ||
| - id: run-tests | ||
| name: "Run tests" | ||
| run: | | ||
| # note: this only runs the fast tests | ||
| pytest -n auto --pyargs openfe openfecli |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| name: Test Self-Hosted Runner | ||
| on: | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| start-aws-runner: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| id-token: write | ||
| contents: read | ||
| outputs: | ||
| mapping: ${{ steps.aws-start.outputs.mapping }} | ||
| steps: | ||
| - name: Configure AWS credentials | ||
| uses: aws-actions/configure-aws-credentials@v4 | ||
| with: | ||
| role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS | ||
| aws-region: us-east-2 | ||
| - name: Create cloud runner | ||
| id: aws-start | ||
| uses: omsf-eco-infra/gha-runner@v0.2.0 | ||
| with: | ||
| provider: "aws" | ||
| action: "start" | ||
| aws_image_id: ami-0b7f661c228e6a4bb | ||
| aws_instance_type: g4dn.xlarge | ||
| aws_region_name: us-east-2 | ||
| aws_home_dir: /home/ubuntu | ||
| env: | ||
| GH_PAT: ${{ secrets.GH_PAT }} | ||
|
|
||
| self-hosted-test: | ||
| runs-on: self-hosted | ||
| timeout-minutes: 720 # 12 hours | ||
| defaults: | ||
| run: | ||
| shell: bash -leo pipefail {0} | ||
| env: | ||
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | ||
|
|
||
| needs: | ||
| - start-aws-runner | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - name: Print disk usage | ||
| run: "df -h" | ||
|
|
||
| - name: Print Docker details | ||
| run: "docker version || true" | ||
|
|
||
| - name: Check for nvidia-smi | ||
| run: "nvidia-smi" | ||
|
|
||
| - name: "Setup Micromamba" | ||
| uses: mamba-org/setup-micromamba@v1 | ||
| with: | ||
| micromamba-version: '1.5.6-0' | ||
| environment-file: environment.yml | ||
| environment-name: openfe_env | ||
| condarc: | | ||
| channels: | ||
| - conda-forge | ||
| - openeye | ||
| create-args: >- | ||
| espaloma_charge==0.0.8 | ||
| openeye-toolkits | ||
| - name: "Check if OpenMM can get a GPU" | ||
| run: python -m openmm.testInstallation | ||
|
|
||
| - name: "Install GUFE from main@HEAD" | ||
| run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main | ||
|
|
||
| - name: "Install" | ||
| run: python -m pip install --no-deps -e . | ||
|
|
||
| - name: "Test imports" | ||
| run: | | ||
| # if we add more to this, consider changing to for + env vars | ||
| python -Ic "import openfe; print(openfe.__version__)" | ||
| - name: "Environment Information" | ||
| run: | | ||
| micromamba info | ||
| micromamba list | ||
| pip list | ||
| - name: Test OE License & Write License to File | ||
| env: | ||
| OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }} | ||
| run: | | ||
| echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE} | ||
| python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'" | ||
| - name: "Run tests" | ||
| env: | ||
| # Set the OFE_SLOW_TESTS to True if running a Cron job | ||
| OFE_SLOW_TESTS: "true" | ||
| DUECREDIT_ENABLE: 'yes' | ||
| OFE_INTEGRATION_TESTS: TRUE | ||
| run: | | ||
| pytest -n 4 -v --durations=10 | ||
| stop-aws-runner: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| id-token: write | ||
| contents: read | ||
| needs: | ||
| - start-aws-runner | ||
| - self-hosted-test | ||
| if: ${{ always() }} | ||
| steps: | ||
| - name: Configure AWS credentials | ||
| uses: aws-actions/configure-aws-credentials@v4 | ||
| with: | ||
| role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS | ||
| aws-region: us-east-2 | ||
| - name: Stop instances | ||
| uses: omsf-eco-infra/gha-runner@v0.2.0 | ||
| with: | ||
| provider: "aws" | ||
| action: "stop" | ||
| instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }} | ||
| aws_region_name: us-east-2 | ||
| env: | ||
| GH_PAT: ${{ secrets.GH_PAT }} |
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